How to reduce mesh vertices to obtain homogenous density while maintaining manifoldness
Well, I think I may have found a nice way to solve my own issue using the remesh tool itself:
Using the &quot;QuadriFlow Remesh&quot; with the &quot;Edge Length&quot; mode set to the desired value, or using the &quot;Vertex Remesh&quot; with the &quot;Voxel Size&quot; set to the desired value, produces pretty and homogeneous meshes while maintaining manifoldness.
Example:

Starting with a UV Sphere, which has a vertex density not so homogeneous


Apply a &quot;QuadriFlow Remesh&quot; with the &quot;Edge Length&quot; mode


The mesh gets a more homogeneous vertex density




Using the &quot;Vertex Remesh&quot; with the &quot;Voxel Size&quot; set to the desired value


will result in an also nice mesh:



The other remesh settings, may also produce nice results.
(Anyway, I still think that the merge by distance has some kind of bug, or else it must be used carefully. Edit: it's not a bug, it's expected behavior)